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SELECT VARIANTS FROM EXCLUDE VARIANTS FROM
INDIVIDUALS:

SNP LIST:
 GROUPS:

SAVED GENE LIST:

GENE LIST:
INDIVIDUALS:

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 EXCLUDE GROUPS:

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OMIM:
CLINICAL GENOMICS DATABASE:
HGMD:
MUTATION TYPE:
 CHR:

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VARIANT EFFECT FUNCTIONAL CLASS IMPACT
DBSNP BUILD:


EXCLUDE VARIANTS AT VARISNP 		READ DEPTH:

QUAL:
VARIANTS PER GENE:
SHOW ONLY VARIANTS PRESENT IN COMMON GENES BETWEEN ALL THE INDIVIDUALS SELECTED
SHOW ONLY VARIANTS AT EXACTLY SAME POSITION BETWEEN ALL THE INDIVIDUALS SELECTED
EXCLUDE ALL VARIANTS PRESENT IN LATEST DBSNP BUILD
SHOW ONLY VARIANTS PRESENT AT HGMD

FREQUENCIES

1000 GENOMES FREQUENCY

EXCLUDE ALL VARIANTS PRESENT IN 1000GENOMES 		DBSNP FREQUENCY

EXCLUDE ALL VARIANTS PRESENT IN DBSNP 		ESP6500 FREQUENCY

EXCLUDE ALL VARIANTS PRESENT IN EXOME SEQUENCING PROJECT

SCORES

SIFT SCORE

EXCLUDE VARIANTS WITHOUT SIFT SCORE 		POLYPHEN2 SCORE

EXCLUDE VARIANTS WITHOUT POLYPHEN SCORE
CADD

EXCLUDE VARIANTS WITHOUT CADD SCORE 		MCAP

EXCLUDE VARIANTS WITHOUT M-CAP SCORE
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+ Genes 2

Genes:
KIT, PDGFRA,

+ Genes associated with diseases 2

Genes at Omim

KIT, PDGFRA,
KIT Gastrointestinal stromal tumor, familial, 606764 (3)
Germ cell tumors, somatic, 273300 (3)
Leukemia, acute myeloid, 601626 (3)
Mastocytosis, cutaneous, 154800 (3)
Mastocytosis, systemic, somatic, 154800 (3)
Piebaldism, 172800 (3)
PDGFRA Gastrointestinal stromal tumor, somatic, 606764 (3)
Hypereosinophilic syndrome, idiopathic, resistant to imatinib, 607685 (3)

Genes at Clinical Genomics Database

KIT, PDGFRA,
KIT Gastrointestinal stromal tumor
PDGFRA Gastrointestinal stromal tumor

Genes at HGMD

Summary

Number of Variants: 21
Number of Genes: 2

Export to: CSV
  • Page 1 of 1

KIT
Omim - GeneCards - NCBI
Options Individual Chr
 RsId
 Pos
 Qual
 Ref
 Alt
 Filter Gen
 Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View valid-000001933_mtdepth-216 smcounter cut 4 . 55604693 88.0 C A PrimerCP 0/1 0 SYNONYMOUS_CODING LOW None None None None None None None KIT|0.689603428|8.78%
View valid-000001933_mtdepth-216 smcounter cut 4 rs3733542
dbSNP Clinvar 		55602765 323.0 G C PASS 0/1 0 SYNONYMOUS_CODING LOW None 0.16414 0.16410 0.19307 None None None None None None KIT|0.689603428|8.78%

PDGFRA
Omim - GeneCards - NCBI
Options Individual Chr
 RsId
 Pos
 Qual
 Ref
 Alt
 Filter Gen
 Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View valid-000001933_mtdepth-216 smcounter cut 4 rs151259376
dbSNP Clinvar 		55131129 170.0 G A PASS 0/1 0 SYNONYMOUS_CODING LOW None 0.00599 0.00599 0.00892 None None None None None None None
View valid-000001933_mtdepth-216 smcounter cut 4 rs4358459
dbSNP Clinvar 		55133726 99.0 T G PASS 0/1 0 SYNONYMOUS_CODING LOW None 0.23423 0.23420 0.16323 None None None None None None None
View valid-000001933_mtdepth-216 smcounter cut 4 rs35597368
dbSNP Clinvar 		55139771 202.0 T C PASS 0/1 0 NON_SYNONYMOUS_CODING MODERATE None 0.19928 0.19930 0.14432 0.24 0.00 None None None None None None None
View valid-000001933_mtdepth-216 smcounter cut 4 rs1873778
dbSNP Clinvar 		55141055 1180.0 A G PASS 1/1 0 SYNONYMOUS_CODING LOW None 0.95767 0.95770 0.04114 None None None None None None None
View valid-000001933_mtdepth-216 smcounter cut 4 rs10028020
dbSNP Clinvar 		55143577 295.0 G A PASS 0/1 0 SYNONYMOUS_CODING LOW None 0.22804 0.22800 0.16615 None None None None None None None
View valid-000001933_mtdepth-216 smcounter cut 4 rs2228230
dbSNP Clinvar 		55152040 459.0 C T PASS 0/1 0 SYNONYMOUS_CODING LOW None 0.24042 0.24040 0.19829 None None None None None None None
View valid-000001933_mtdepth-216 smcounter cut 4 rs2229307
dbSNP Clinvar 		55130078 158.0 T C PASS 0/1 0 SYNONYMOUS_CODING LOW None 0.23622 0.23620 0.16500 None None None None None None None
View valid-000001933_mtdepth-216 smcounter cut 4 . 55127494 99.0 C T PASS 0/1 0 SYNONYMOUS_CODING LOW None None None None None None None None
View valid-000001933_mtdepth-216 smcounter cut 4 rs7685117
dbSNP Clinvar 		55161391 802.0 T C PASS 1/1 0 SYNONYMOUS_CODING LOW None 0.99720 0.99720 0.00323 None None None None None None None
Omim - GeneCards - NCBI
Options Individual Chr
 RsId
 Pos
 Qual
 Ref
 Alt
 Filter Gen
 Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View valid-000001933_mtdepth-216 smcounter cut 4 rs2307049
dbSNP Clinvar 		55130154 33.0 G A PASS 0/1 0 None None None 0.23562 0.23560 None None None None None None None
View valid-000001933_mtdepth-216 smcounter cut 4 . 55592268 24.0 T A LowQ;R2CP 0/1 0 None None None None None None None None None KIT|0.689603428|8.78%
View valid-000001933_mtdepth-216 smcounter cut 4 rs17084713
dbSNP Clinvar 		55597458 79.0 A G PASS 0/1 0 None None None 0.02616 0.02616 0.02738 None None None None None None KIT|0.689603428|8.78%
View valid-000001933_mtdepth-216 smcounter cut 4 rs11935331
dbSNP Clinvar 		55599129 273.0 T A PASS 0/1 0 None None None 0.19070 0.19070 None None None None None None KIT|0.689603428|8.78%
View valid-000001933_mtdepth-216 smcounter cut 4 rs4864921
dbSNP Clinvar 		55599159 503.0 G A PASS 0/1 0 None None None 0.32089 0.32090 1.86 0.00 0.10928 T None None None None KIT|0.689603428|8.78%
View valid-000001933_mtdepth-216 smcounter cut 4 rs1008658
dbSNP Clinvar 		55599436 163.0 T C PASS 0/1 0 None None None 0.50479 0.50480 None None None None None None KIT|0.689603428|8.78%
View valid-000001933_mtdepth-216 smcounter cut 4 rs1907820
dbSNP Clinvar 		55144447 172.0 T C PASS 1/1 0 None None None 0.95288 0.95290 None None None None None None None
View valid-000001933_mtdepth-216 smcounter cut 4 . 55602792 32.0 C A LSM;LowQ;PrimerCP 0/1 0 None None None None None None None None None KIT|0.689603428|8.78%
View valid-000001933_mtdepth-216 smcounter cut 4 rs3830355
dbSNP Clinvar 		55151958 126.0 T TA PASS 0/1 0 None None None 0.71386 0.71390 0.25032 None None None None None None None
View valid-000001933_mtdepth-216 smcounter cut 4 . 55602878 21.0 G A LowQ 0/1 0 None None None None None None None None None KIT|0.689603428|8.78%
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